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Governor Deval Patrick left scant hope that Daniel A. Grabauskas will retain his job as general manager of the MBTA, saying yesterday that he has serious concerns about “the competence of the leadership and the adequacy of the management’’ at the troubled transit agency.

“We’ve had two serious accidents within a short time frame,’’ said Patrick, stopping just short of requesting Grabauskas’s ouster. “We’ve got serious fiscal issues at the T, so serious that even with some infusion of new state dollars they are still considering a fare increase, something that could not come at a worse time.’’

Patrick’s statements were but one side of a sharpening debate over Grabauskas’s future heading one of the nation’s largest public transit agencies. Legislative leaders, including both the House speaker and the Senate president, publicly lauded Grabauskas yesterday, with some questioning Patrick’s motives. The MBTA board itself may also be divided.

“He’s been a good head of the T,’’ said Senate President Therese Murray, speaking at a lunch forum on the Boston waterfront. “But he’s from a different party, and the governor and his people would like a different person in there.’’

The head of the House Transportation Committee took it a step further, joining his Senate counterpart in accusing the Patrick administration of “gamesmanship.’’

“What I am watching unfold here strikes me as very political,’’ said Representative Joseph F. Wagner, a Chicopee Democrat. “I have a concern that the focus of the administration should be to try and move forward and implement the new transportation reform law.’’

House Speaker Robert A. DeLeo issued a written statement describing Grabauskas as “responsive and attentive.’’

The acrimonious debate - set off by a highly critical letter from three T board members this week - will probably spill into the end of next week, when the board is scheduled to meet with Grabauskas and discuss his future that Thursday.

Grabauskas yesterday reiterated that he would not resign, then chided Patrick with a famous Ronald Reagan quote.

“Well, there you go again,’’ Grabauskas said in a phone interview last night. “They’re vague and unsubstantiated allegations, and I continue to think, as do many others, that they are politically motivated.’’

Several legislators and transit advocates said they worry that the coarsening dialogue will undermine efforts to rebuild the state’s dysfunctional transportation system and distract attention from the Massachusetts Bay Transportation Authority’s crippling debt. “Changing the face on the poster doesn’t make the train run on time,’’ said Christopher Hart, a transit consultant and activist who has both fought the T over access for disabled riders and consulted for the agency. “Fixing the tracks, fixing the systems, buying new trains, providing new training for the staff - that will actually make the trains run on time.’’

Three of the eight MBTA board members signed the letter, delivered Tuesday, accusing Grabauskas of losing “focus and commitment’’ to safety and efficiency at the agency. They wrote that they had lost confidence in his ability to lead. The letter followed two high-profile Green Line crashes within a year of each other and a highly critical report this month from the National Transportation Safety Board about one of the crashes.

But Grabauskas’s allies point to accomplishments over his four-year tenure, saying he has done significant work in making the system more accessible to disabled riders, implemented an automated fare-payment system, and increased the size of the transit police force and the number of security cameras. Grabauskas oversaw record ridership months through 2008 and part of 2009.

The T board is chaired by Patrick’s transportation secretary, James A. Aloisi Jr., who clashed publicly with Grabauskas in recent weeks after what started as a cooperative relationship.

In his comments, Patrick did not note that Aloisi has backed a substantial fare increase and that Aloisi and the T board directed Grabauskas to raise fares at a public meeting.

One board member, who talked on the condition of anonymity, said yesterday that the board appears divided over whether to fire Grabauskas or negotiate an exit with him, given the apparent desire of Patrick to put his own leader in the job.

Aside from the three board members who signed the letter and chairman Aloisi, two others have told the Globe they either back Grabauskas or want to hear his side. Two remaining board members did not return calls to their homes and cellphones yesterday.

Grabauskas, a Republican who lost the election for state treasurer in 2002, is a rare holdover from the Romney administration. He has long been something of an outsider in the Patrick administration and is often mentioned as a potential candidate for statewide office.

He has 9 1/2 months remaining on a contract with the T that will pay him $255,000 this year. He was due $280,000, but deferred two contractual pay increases under pressure from the Patrick administration. The contract requires that he be paid his remaining salary and benefits if fired, unless for a cause “limited to actions by Grabauskas involving gross and deliberate malfeasance, gross negligence, or final conviction of a crime of moral turpitude.’’

Aloisi, before a public appearance at the State House yesterday, said he has not been satisfied in general with the T over the past several years. “This is about getting it right. And attempts to change the discussion, frankly, by throwing politics into it or throwing personality into it, that’s not right, it’s not fair,’’ he said.

The MBTA board is set to be disbanded after its October meeting. A new board, part of an overhaul of all state transportation agencies, will be appointed by the governor, but will have to include professional planners, financial specialists, and a civil engineer. Wagner and Senator Steven A. Baddour, a Methuen Democrat who is cochairman of the joint transportation committee, say the professional nature of the new board is crucial to reducing politics in the state’s transportation system and will be set back significantly if true professionals are not appointed.

Several transit advocates said damage has already been done to the T, voicing concern that infighting is particularly harmful during an already volatile period.

Taisha O’Bryant, chairwoman of the T Riders Union, expressed dismay with Grabauskas and the board, saying they are fighting with each other rather than advocating for riders. “Why aren’t the T board members stepping out and saying how they’re going to stop the fare increase?’’ she said.

Staff writer Matthew Viser contributed to this report. Noah Bierman can be reached at nbierman@globe.com.